4XFE

Crystal structure of a TRAP periplasmic solute binding protein from Pseudomonas putida F1 (Pput_1203), Target EFI-500184, with bound D-glucuronate

• PDB DOI: https://doi.org/10.2210/pdb4XFE/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudomonas putida ND6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-26 Released: 2015-01-28 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Crystal structure of a TRAP periplasmic solute binding protein from Pseudomonas putida F1 (Pput_1203), Target EFI-500184, with bound D-glucuronate

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.33 kDa 
• Atom Count: 2,739 
• Modelled Residue Count: 306 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP dicarboxylate transporter subunit DctP	A	341	Pseudomonas putida ND6	Mutation(s): 0  Gene Names: YSA_07416
UniProt
Find proteins for I3UZ52 (Pseudomonas putida ND6) Explore I3UZ52  Go to UniProtKB:  I3UZ52

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	C [auth A]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
BDP	B [auth A]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.001	α = 90
b = 35.054	β = 99.54
c = 60.833	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Experimental preparation
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary